When the U.S. Supreme Court upheld the Affordable Care Act, the Special Needs Network, a nonprofit group advocating the interests of special-needs families, praised the law for ensuring that those with pre-existing conditions have health insurance.

Starting in 2013, members of the same community may be smarting from two little-known changes imposed by the health care law that some say will hit families with high medical expenses, especially those with special-needs children.

Parents of special-needs children and others with high medical expenses said the changes mean that they’ll have to pay more out of pocket for their child’s treatment and pay higher taxes.

The changes that take effect in January will:

Cap annual contributions to flexible spending accounts established by employees with pretax money to pay for unreimbursed medical expenses at $2,500.

Currently, there isn’t a statutory limit on how much you can contribute to an FSA, but most employers impose an annual contribution limit of $5,000, said Paul Fronstin, director of the Health Research and Education Program at the Employee Benefit Research Institute.

Increase the threshold for the itemized deduction for unreimbursed medical expenses from 7.5 percent of adjusted gross income to 10 percent of adjusted gross income.

That change won’t apply to those age 65 and older until 2017.

“This is a travesty, really, for those of us who have children with special needs,” said Brenda Batts, owner of Focus on the Future Training Center in Plano, a school for autistic children. “The cost of raising a neurotypical child [a child who’s not autistic] is $290,000 [over his or her lifetime]. The average cost of raising a child with autism is $3.2 million over his or her lifespan.

“Most of our kids, especially if they have moderate to severe autism, will be the ones hardest hit with this change.”

Therapy’s cost

Many special-needs children require regular therapy, said Batts, who has a 21-year-old son who’s autistic. The costs run an average of $75 to $150 an hour for speech therapy, occupational therapy and physical therapy, she said.

“As it is now, insurance only covers certain therapies,” Batts said. “If they cover it, they only cover a certain amount of sessions, so with these changes, it’s really going to hurt the families.”

And those are expenses for therapies only. There are also medications that autistic children need.

“Most of the kids with autism take a lot of medications,” Batts said.

They’re mostly for behavioral medication, but many autistic kids have seizure disorders, she said.

“The medication is so expensive,” Batts said. “We’re talking about certain medications running up to $400, $500 a month for kids who do not have insurance.”

Tom Murphy, certified financial planner at Murphy & Sylvest LLC, created examples of how the two changes will work.

The flex plan change: “I think the FSA change is the big deal,” Murphy said. “If you know you will spend $30,000 in care for a special-needs child, under the existing rules you can put $30,000 in an FSA and have it all be pretax.”

“Starting Jan. 1, however, you will have to pay any amount over $2,500 out of pocket after tax,” he said. “If you are a middle-income taxpayer with an AGI of $50,000 per year [which puts you in the 25 percent tax bracket], that means you will pay about $625 more in taxes starting in 2013.”

The itemized deduction of medical expenses: Say the same middle-income taxpayer has unreimbursed medical expenses of $10,000. The increase in the threshold for itemizing from 7.5 percent to 10 percent will result in a tax increase of about $312, Murphy said.

‘Huge for families’

“Although these amounts are small by some standards, they are huge for families desperately trying to care for a child,” Murphy said.

For David Gee, whose 6-year-old son, John, is autistic, the impact of the rule changes is a looming shadow.

He’s been unemployed for 14 months, so he doesn’t have a flex plan account. He was laid off from his job selling financing for major company purchases, and his family has been living off savings.

“We had to shut all the therapy off, pay all the bills and just call it a day,” Gee said.

John is getting some speech and occupational therapy at school, but he needs three to five hours a week of therapies, Gee said.

When he returns to work, his family will be hurt first by the flex plan change when they pay for John’s therapies.

“The day that I become employed, the flex plan’s going to hurt immediately because we’ll overrun that [$2,500] in a number of months,” Gee said. “We will cross that threshold where we’ll be paying after-tax money sooner rather than later.”

The Gees will easily have enough medical expenses to deduct from their taxes, but the 33 percent increase in the threshold — from 7.5 percent to 10 percent — will hurt.

“That’s significant,” Gee said. “There’s pain associated with that. We’ve lost the deduction for a significant amount of our outflow, and that hurts as well.”

Although there’s nothing you can do about the $2,500 limit on flex plan accounts, there is something you can do to lessen the impact of the higher threshold to deduct medical expenses.

“If you have some flexibility as to when you incur the medical expenses, try to lump them every other year so that you tend to help ensure that you get maximum expenses over the percentage limit,” said Mark Luscombe, principal analyst at CCH, which publishes tax information.

“Rather than just having an even amount each year, which might tend to always fall under the 7.5 percent or the 10 percent, if you put them every other year then you increase the amount in that year and are likely to have expenses that would exceed the 10 percent or the 7.5 percent,” he said.